R Notebook

Diversity

overall diversity

raw diversity

Change in diversity

##            1-1       1-3      10-1      10-3      10-5      11-1      11-3
## 1-3  0.9089446                                                            
## 10-1 1.0000000 0.9977528                                                  
## 10-3 0.9987315 0.9991164 0.9771632                                        
## 10-5 0.9976303 0.9991771 0.9836257 0.9740557                              
## 11-1 0.9980691 0.9979904 0.9995444 0.9981333 0.9968371                    
## 11-3 0.9985714 0.9994996 0.9994137 0.9986295 0.9983022 0.9477937          
## 11-5 0.9987356 0.9986937 0.9992777 0.9981553 0.9985378 0.9462180 0.9340586
## 12-1 0.9994877 0.9989192 0.9993579 0.9995100 0.9981884 0.9991172 1.0000000
## 12-3 0.9993146 0.9996449 1.0000000 0.9986698 0.9981096 0.9993811 0.9978118
## 12-5 0.9984116 0.9993032 0.9980062 0.9971085 0.9980699 0.9972461 0.9983455
## 13-1 0.9986159 0.9975799 0.9994360 0.9982273 0.9971116 0.9987908 0.9984936
## 13-5 0.9991500 0.9991117 0.9989788 0.9971335 0.9988501 0.9984999 0.9990813
## 14-1 1.0000000 0.9982358 0.9964476 0.9989424 0.9970845 0.9985819 1.0000000
## 14-5 0.9994722 0.9988846 0.9973333 0.9994958 0.9976750 0.9981884 0.9982543
## 15-1 0.9980952 0.9988112 0.9991033 0.9977892 0.9979174 0.9976178 0.9987750
## 15-5 0.9992857 0.9977765 0.9987529 0.9975770 0.9973822 0.9967882 0.9988567
## 16-1 0.9986413 0.9976264 0.9977943 0.9973879 0.9987825 0.9996034 0.9990157
## 16-5 0.9986311 0.9980861 0.9994435 0.9986845 0.9971399 0.9976048 0.9995038
## 17-1 0.9989227 0.9977208 0.9993160 0.9994860 0.9990533 0.9990783 1.0000000
## 17-5 0.9979371 0.9983673 0.9987051 0.9990138 0.9986333 0.9991121 0.9988656
## 18-1 0.9993286 1.0000000 0.9990868 0.9987330 0.9988542 0.9977815 1.0000000
## 18-5 0.9983682 0.9994243 1.0000000 1.0000000 0.9980902 1.0000000 0.9987970
## 19-1 0.9982517 0.9990853 0.9994719 0.9995793 0.9980346 0.9988468 0.9985795
## 19-5 0.9977873 0.9990202 0.9996389 0.9981553 0.9976605 0.9968364 0.9963180
## 2-1  0.9991830 0.9987215 0.9975651 0.9984233 0.9985207 0.9992758 0.9982394
## 2-3  0.9979724 0.9991542 1.0000000 0.9972603 0.9985305 0.9982011 0.9978166
## 2-5  0.9986652 0.9990680 0.9989207 0.9982880 0.9984022 0.9980476 0.9975863
## 20-1 0.9978061 1.0000000 0.9973468 0.9987331 0.9984221 0.9984571 0.9985735
## 20-5 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 21-1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 22-5 0.9984759 0.9984146 0.9982063 0.9970518 0.9965284 0.9986385 0.9983663
## 23-1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 23-5 0.9989373 0.9988977 1.0000000 0.9986264 0.9980513 0.9980870 0.9992444
## 24-1 0.9979522 0.9978787 0.9984224 0.9986751 0.9971751 0.9984585 0.9978214
## 24-5 0.9977439 0.9988272 0.9995585 0.9981808 0.9989710 0.9993273 0.9987920
## 3-1  0.9990606 0.9985203 0.9953877 0.9986474 0.9966457 0.9983623 0.9989759
## 3-3  0.9994660 0.9988707 1.0000000 1.0000000 0.9995302 0.9986276 0.9994106
## 3-5  0.9995022 0.9979030 1.0000000 0.9990467 0.9995585 0.9978471 1.0000000
## 5-1  0.9992687 1.0000000 0.9989723 0.9993134 0.9987681 0.9988102 1.0000000
## 5-3  0.9977624 0.9990624 0.9994565 1.0000000 0.9979924 0.9992151 0.9985426
## 5-5  0.9969512 0.9977185 0.9975105 0.9964836 0.9958592 0.9977050 0.9979604
## 6-1  0.9988343 0.9987864 0.9981643 0.9984977 0.9978795 0.9986145 0.9974974
## 6-3  0.9992393 0.9980218 0.9982099 0.9985283 0.9972270 0.9983008 0.9995923
## 6-5  1.0000000 0.9982222 0.9985658 0.9989350 0.9985330 0.9995244 0.9987601
## 7-1  0.9990764 0.9995155 0.9983060 0.9982258 0.9991741 0.9991932 0.9994974
## 7-3  0.9995762 0.9977857 0.9984733 0.9979579 0.9988530 0.9992518 0.9981681
## 7-5  0.9993176 1.0000000 0.9990663 0.9987134 0.9994191 0.9994379 0.9992245
## 8-1  0.9986979 0.9986379 0.9984289 0.9979106 0.9980469 0.9988539 0.9985902
## 8-3  0.9995226 0.9984947 1.0000000 0.9986261 0.9982982 0.9987542 0.9994788
## 8-5  0.9990449 1.0000000 1.0000000 0.9990838 1.0000000 0.9991693 0.9989572
## 9-1  0.9982006 1.0000000 0.9983593 0.9974048 0.9975797 0.9980288 0.9980459
## 9-3  0.9993793 0.9986751 0.9983559 1.0000000 0.9994644 0.9989608 0.9993031
## 9-5  0.9995267 1.0000000 1.0000000 0.9995459 0.9983115 0.9983515 0.9979350
##           11-5      12-1      12-3      12-5      13-1      13-5      14-1
## 1-3                                                                       
## 10-1                                                                      
## 10-3                                                                      
## 10-5                                                                      
## 11-1                                                                      
## 11-3                                                                      
## 11-5                                                                      
## 12-1 0.9989435                                                            
## 12-3 0.9976350 0.9375482                                                  
## 12-5 0.9962225 0.9365663 0.8700733                                        
## 13-1 0.9977087 0.9994576 0.9992881 0.9986042                              
## 13-5 0.9978398 0.9995071 0.9993322 0.9984389 0.9688127                    
## 14-1 0.9992564 0.9986468 0.9995908 0.9987287 0.9988190 0.9994678          
## 14-5 0.9992811 1.0000000 0.9992115 0.9987579 0.9983203 0.9984783 0.8908835
## 15-1 0.9965836 0.9986962 0.9975513 0.9972666 0.9964236 0.9977794 0.9986053
## 15-5 0.9972881 0.9991922 0.9982568 0.9975664 0.9985138 0.9989572 0.9995701
## 16-1 0.9980617 0.9989384 0.9985965 0.9988477 0.9976185 0.9982495 0.9976932
## 16-5 0.9987009 1.0000000 0.9978825 0.9990746 0.9990398 0.9982367 0.9982533
## 17-1 0.9974490 0.9993475 0.9991995 0.9997492 0.9988558 0.9989656 0.9985533
## 17-5 0.9989386 0.9981424 0.9992251 0.9985258 0.9994537 0.9990079 0.9972696
## 18-1 0.9991586 1.0000000 0.9995308 0.9997238 1.0000000 1.0000000 0.9980305
## 18-5 0.9996332 0.9993397 0.9995969 0.9989923 0.9994220 0.9989559 0.9992671
## 19-1 0.9984254 0.9984725 0.9982935 0.9972845 1.0000000 0.9995772 0.9988975
## 19-5 0.9972846 0.9992957 0.9973722 0.9958447 0.9996727 0.9975312 0.9973973
## 2-1  0.9973018 0.9990584 0.9990291 0.9960690 0.9991451 0.9980198 0.9994934
## 2-3  0.9970180 0.9985994 0.9983912 0.9976071 0.9978791 0.9980338 0.9984940
## 2-5  0.9984051 0.9989602 0.9982696 0.9990864 0.9985975 0.9978490 0.9994361
## 20-1 0.9971577 0.9994885 0.9972612 0.9984127 0.9995393 0.9987267 1.0000000
## 20-5 0.9995099 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 21-1 1.0000000 1.0000000 1.0000000 0.9996994 1.0000000 1.0000000 1.0000000
## 22-5 0.9985763 0.9986959 0.9975509 0.9981075 0.9996025 0.9974088 0.9981400
## 23-1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 23-5 0.9986525 0.9971989 0.9985570 0.9967703 0.9985264 0.9986207 0.9991486
## 24-1 0.9968566 1.0000000 0.9980403 0.9972337 0.9971646 0.9996674 0.9967427
## 24-5 0.9980265 0.9978591 0.9981826 0.9974950 0.9972560 0.9985383 0.9981698
## 3-1  0.9980109 0.9983380 0.9985565 0.9992958 1.0000000 0.9986401 0.9987915
## 3-3  0.9981884 0.9987084 0.9988069 0.9985013 0.9988662 0.9979482 0.9992849
## 3-5  0.9979285 0.9976261 0.9996228 0.9985507 0.9994738 0.9990412 0.9993485
## 5-1  0.9991131 1.0000000 0.9995024 0.9997142 1.0000000 1.0000000 0.9988808
## 5-3  0.9987188 0.9989532 0.9979141 0.9977093 0.9995296 0.9995674 0.9971599
## 5-5  0.9977756 0.9996955 0.9971765 0.9977348 0.9977140 0.9989145 0.9984046
## 6-1  0.9982664 0.9982218 0.9990670 0.9982995 0.9987830 0.9981136 0.9980948
## 6-3  0.9980094 0.9982646 0.9966371 0.9974790 0.9992065 0.9977827 0.9990719
## 6-5  0.9988791 1.0000000 0.9995886 0.9987245 0.9982148 0.9989282 0.9992395
## 7-1  0.9980347 0.9989139 0.9996438 0.9974398 0.9990277 0.9982163 0.9988176
## 7-3  0.9990761 0.9990174 0.9986673 0.9973277 0.9991115 0.9991792 0.9989393
## 7-5  1.0000000 1.0000000 1.0000000 0.9994439 1.0000000 0.9980551 1.0000000
## 8-1  0.9981200 0.9984848 0.9996606 0.9988726 0.9990890 0.9987400 0.9978142
## 8-3  0.9976526 0.9994352 0.9978074 0.9983434 0.9994965 0.9995395 0.9987658
## 8-5  0.9993292 0.9994350 0.9981725 0.9981065 0.9994963 0.9986181 0.9993827
## 9-1  0.9983925 0.9989468 0.9993019 0.9983923 0.9990541 0.9986957 0.9959977
## 9-3  0.9983990 0.9992230 0.9991123 0.9991983 0.9993344 1.0000000 1.0000000
## 9-5  0.9973338 0.9983231 0.9989111 0.9981150 0.9990022 0.9981735 0.9981696
##           14-5      15-1      15-5      16-1      16-5      17-1      17-5
## 1-3                                                                       
## 10-1                                                                      
## 10-3                                                                      
## 10-5                                                                      
## 11-1                                                                      
## 11-3                                                                      
## 11-5                                                                      
## 12-1                                                                      
## 12-3                                                                      
## 12-5                                                                      
## 13-1                                                                      
## 13-5                                                                      
## 14-1                                                                      
## 14-5                                                                      
## 15-1 0.9973256                                                            
## 15-5 0.9987596 0.9514131                                                  
## 16-1 0.9978100 0.9976535 0.9985359                                        
## 16-5 1.0000000 0.9972446 0.9974222 0.9350130                              
## 17-1 1.0000000 0.9972795 0.9991598 0.9988817 0.9966140                    
## 17-5 0.9980738 0.9982517 0.9991880 0.9962587 1.0000000 0.8716683          
## 18-1 0.9990975 0.9994561 0.9995034 1.0000000 0.9985765 0.9990654 0.9982646
## 18-5 0.9986273 0.9995429 0.9983069 1.0000000 1.0000000 1.0000000 1.0000000
## 19-1 0.9973774 0.9988623 0.9982219 0.9986486 0.9963694 0.9983944 0.9974372
## 19-5 0.9978433 0.9980071 0.9972881 0.9967695 0.9983761 0.9974490 0.9968158
## 2-1  0.9990322 0.9992849 0.9979812 0.9983193 0.9987307 0.9985211 0.9990526
## 2-3  0.9985608 0.9968028 0.9966555 0.9987490 0.9987403 0.9990227 0.9981212
## 2-5  0.9994641 0.9996149 0.9971135 0.9990824 0.9976884 0.9978118 0.9994766
## 20-1 0.9984190 0.9984779 0.9985730 1.0000000 0.9968102 0.9978489 0.9969104
## 20-5 1.0000000 1.0000000 0.9994037 1.0000000 1.0000000 1.0000000 1.0000000
## 21-1 1.0000000 0.9987051 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 22-5 0.9982167 0.9963007 0.9980943 0.9980442 0.9992126 0.9990930 0.9986885
## 23-1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 23-5 0.9983617 0.9959016 0.9973110 0.9985481 0.9978090 0.9970876 0.9959775
## 24-1 0.9984304 0.9987801 0.9971048 0.9989518 0.9982428 1.0000000 0.9984574
## 24-5 0.9995610 0.9986704 0.9981153 0.9984565 0.9984466 0.9995536 0.9995694
## 3-1  0.9994278 0.9983858 0.9981153 0.9980592 0.9990218 0.9994150 1.0000000
## 3-3  0.9993293 0.9995499 1.0000000 0.9988917 1.0000000 1.0000000 0.9993487
## 3-5  1.0000000 0.9983036 0.9976313 1.0000000 0.9979215 0.9981126 1.0000000
## 5-1  1.0000000 0.9994174 0.9994713 0.9984609 0.9992206 0.9968354 1.0000000
## 5-3  0.9994603 0.9992259 0.9989125 0.9995384 0.9981395 0.9961433 0.9989460
## 5-5  0.9990702 0.9964620 0.9980639 0.9974576 0.9974457 0.9959228 0.9978600
## 6-1  0.9981752 0.9989735 0.9983858 0.9988026 0.9987947 0.9990715 0.9982115
## 6-3  0.9995551 0.9979852 0.9984142 0.9972667 0.9996070 0.9972845 0.9986911
## 6-5  0.9985790 0.9995323 0.9987030 0.9988379 0.9988266 0.9985396 0.9986226
## 7-1  0.9977578 0.9996023 0.9992564 0.9985697 0.9985584 0.9994273 0.9983593
## 7-3  0.9994944 0.9981540 0.9989596 0.9978180 0.9973626 0.9974227 0.9980222
## 7-5  1.0000000 1.0000000 0.9994974 0.9992844 0.9992759 1.0000000 1.0000000
## 8-1  0.9979194 0.9988692 0.9978784 0.9982111 0.9981978 0.9978774 0.9984748
## 8-3  0.9994162 0.9975445 0.9992362 0.9990131 0.9995025 0.9988060 0.9971550
## 8-5  0.9982482 0.9983627 0.9984721 0.9990128 0.9995024 0.9988056 0.9982925
## 9-1  0.9961988 0.9992224 0.9992719 0.9990719 0.9981295 0.9988910 0.9973489
## 9-3  0.9991867 0.9989796 0.9995316 0.9993519 0.9980347 0.9974822 0.9992151
## 9-5  0.9988449 0.9991877 0.9973455 0.9955990 0.9995070 0.9982285 0.9971847
##           18-1      18-5      19-1      19-5       2-1       2-3       2-5
## 1-3                                                                       
## 10-1                                                                      
## 10-3                                                                      
## 10-5                                                                      
## 11-1                                                                      
## 11-3                                                                      
## 11-5                                                                      
## 12-1                                                                      
## 12-3                                                                      
## 12-5                                                                      
## 13-1                                                                      
## 13-5                                                                      
## 14-1                                                                      
## 14-5                                                                      
## 15-1                                                                      
## 15-5                                                                      
## 16-1                                                                      
## 16-5                                                                      
## 17-1                                                                      
## 17-5                                                                      
## 18-1                                                                      
## 18-5 0.9211027                                                            
## 19-1 0.9993340 0.9994596                                                  
## 19-5 0.9995793 0.9981658 0.9241064                                        
## 2-1  0.9993981 0.9980104 0.9983740 0.9973018                              
## 2-3  0.9994046 0.9980281 0.9963680 0.9955271 0.9662623                    
## 2-5  1.0000000 0.9988950 0.9973445 0.9980861 0.9603224 0.9671795          
## 20-1 0.9986600 0.9994570 0.9969446 0.9971577 0.9979600 0.9975699 0.9995557
## 20-5 1.0000000 1.0000000 0.9991416 1.0000000 1.0000000 1.0000000 1.0000000
## 21-1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
## 22-5 0.9983678 0.9967993 0.9977243 0.9971526 0.9982121 0.9964470 0.9973035
## 23-1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9992523 1.0000000
## 23-5 0.9995090 0.9991616 0.9971781 0.9986525 0.9979967 0.9990043 0.9982108
## 24-1 1.0000000 0.9995988 0.9983005 0.9976424 0.9987105 0.9967949 0.9986214
## 24-5 0.9994661 1.0000000 0.9985027 0.9966169 0.9989405 0.9975434 0.9984797
## 3-1  0.9985102 0.9970440 0.9990659 0.9986740 0.9978270 0.9982751 0.9976196
## 3-3  1.0000000 0.9993031 0.9989387 0.9981884 0.9990218 0.9980606 0.9994577
## 3-5  0.9991820 0.9980910 0.9990104 0.9986190 0.9963320 0.9977262 0.9989902
## 5-1  1.0000000 1.0000000 1.0000000 0.9986696 1.0000000 0.9993579 0.9992532
## 5-3  0.9986188 0.9994435 0.9986646 0.9977578 0.9970912 0.9971128 0.9990934
## 5-5  0.9992912 0.9993692 0.9977901 0.9979980 0.9989418 0.9976303 0.9980444
## 6-1  0.9988808 0.9995318 0.9980661 0.9976885 0.9963577 0.9981907 0.9972495
## 6-3  1.0000000 0.9986311 0.9992427 0.9960188 0.9978579 0.9975168 0.9984618
## 6-5  1.0000000 1.0000000 0.9988895 0.9981319 0.9984702 0.9984841 0.9988640
## 7-1  0.9992748 0.9994213 0.9972445 0.9983623 0.9982888 0.9983018 0.9990641
## 7-3  1.0000000 0.9994797 0.9983133 0.9990761 0.9968398 0.9980388 0.9978550
## 7-5  1.0000000 1.0000000 0.9993232 0.9991500 0.9993893 1.0000000 1.0000000
## 8-1  0.9986820 0.9994642 0.9965458 0.9962400 0.9967690 0.9983962 0.9995605
## 8-3  1.0000000 0.9987930 0.9981011 0.9983233 0.9991176 0.9991245 0.9990319
## 8-5  1.0000000 0.9993963 0.9962013 0.9973168 0.9982348 0.9991243 1.0000000
## 9-1  0.9986077 0.9994399 0.9986577 0.9993570 0.9962422 0.9995856 0.9963545
## 9-3  0.9987871 1.0000000 1.0000000 0.9995998 0.9988783 0.9994448 0.9987362
## 9-5  1.0000000 0.9976127 0.9976471 0.9980003 0.9991247 0.9986974 0.9995203
##           20-1      20-5      21-1      22-5      23-1      23-5      24-1
## 1-3                                                                       
## 10-1                                                                      
## 10-3                                                                      
## 10-5                                                                      
## 11-1                                                                      
## 11-3                                                                      
## 11-5                                                                      
## 12-1                                                                      
## 12-3                                                                      
## 12-5                                                                      
## 13-1                                                                      
## 13-5                                                                      
## 14-1                                                                      
## 14-5                                                                      
## 15-1                                                                      
## 15-5                                                                      
## 16-1                                                                      
## 16-5                                                                      
## 17-1                                                                      
## 17-5                                                                      
## 18-1                                                                      
## 18-5                                                                      
## 19-1                                                                      
## 19-5                                                                      
## 2-1                                                                       
## 2-3                                                                       
## 2-5                                                                       
## 20-1                                                                      
## 20-5 0.9930796                                                            
## 21-1 1.0000000 1.0000000                                                  
## 22-5 0.9977165 1.0000000 1.0000000                                        
## 23-1 1.0000000 1.0000000 1.0000000 1.0000000                              
## 23-5 0.9982307 1.0000000 1.0000000 0.9965316 0.9994099                    
## 24-1 0.9979543 1.0000000 1.0000000 0.9969498 1.0000000 0.9971240          
## 24-5 1.0000000 1.0000000 1.0000000 0.9983378 1.0000000 0.9993763 0.9191188
## 3-1  0.9967167 1.0000000 1.0000000 0.9983855 1.0000000 0.9981315 0.9982034
## 3-3  0.9989336 1.0000000 1.0000000 0.9990995 0.9986559 0.9991734 0.9988126
## 3-5  0.9990060 1.0000000 1.0000000 0.9987275 1.0000000 0.9988263 0.9984979
## 5-1  1.0000000 1.0000000 1.0000000 0.9988345 1.0000000 1.0000000 0.9985160
## 5-3  0.9995531 1.0000000 1.0000000 0.9992257 1.0000000 0.9985619 0.9979228
## 5-5  0.9980615 1.0000000 1.0000000 0.9972198 1.0000000 0.9978339 0.9985922
## 6-1  0.9980594 1.0000000 1.0000000 1.0000000 1.0000000 0.9977568 0.9969016
## 6-3  0.9992401 1.0000000 1.0000000 0.9976490 1.0000000 0.9971662 0.9957356
## 6-5  0.9972098 1.0000000 1.0000000 0.9981287 1.0000000 0.9987158 0.9995907
## 7-1  0.9967720 1.0000000 1.0000000 0.9988067 1.0000000 0.9992627 0.9996453
## 7-3  0.9987302 1.0000000 1.0000000 0.9985229 1.0000000 0.9986238 0.9980090
## 7-5  0.9986381 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9995282
## 8-1  0.9978327 1.0000000 1.0000000 0.9981150 1.0000000 0.9982462 0.9993239
## 8-3  0.9985697 1.0000000 0.9990138 0.9979533 1.0000000 0.9988643 0.9978170
## 8-5  0.9976156 1.0000000 1.0000000 0.9979529 1.0000000 0.9977281 0.9985444
## 9-1  0.9986523 1.0000000 1.0000000 0.9972779 1.0000000 0.9978339 0.9986097
## 9-3  0.9987608 0.9979508 1.0000000 0.9994897 1.0000000 0.9990732 0.9991170
## 9-5  0.9985822 1.0000000 1.0000000 0.9979687 1.0000000 0.9973684 0.9978316
##           24-5       3-1       3-3       3-5       5-1       5-3       5-5
## 1-3                                                                       
## 10-1                                                                      
## 10-3                                                                      
## 10-5                                                                      
## 11-1                                                                      
## 11-3                                                                      
## 11-5                                                                      
## 12-1                                                                      
## 12-3                                                                      
## 12-5                                                                      
## 13-1                                                                      
## 13-5                                                                      
## 14-1                                                                      
## 14-5                                                                      
## 15-1                                                                      
## 15-5                                                                      
## 16-1                                                                      
## 16-5                                                                      
## 17-1                                                                      
## 17-5                                                                      
## 18-1                                                                      
## 18-5                                                                      
## 19-1                                                                      
## 19-5                                                                      
## 2-1                                                                       
## 2-3                                                                       
## 2-5                                                                       
## 20-1                                                                      
## 20-5                                                                      
## 21-1                                                                      
## 22-5                                                                      
## 23-1                                                                      
## 23-5                                                                      
## 24-1                                                                      
## 24-5                                                                      
## 3-1  0.9988060                                                            
## 3-3  0.9986702 0.9594320                                                  
## 3-5  0.9991641 0.9645542 0.9483027                                        
## 5-1  0.9988578 0.9991807 0.9989627 1.0000000                              
## 5-3  0.9977082 0.9985629 0.9983616 0.9979670 0.9494721                    
## 5-5  0.9972441 0.9979775 0.9996879 0.9982041 0.9740693 0.9453245          
## 6-1  0.9986473 0.9991758 0.9990783 0.9991329 0.9993994 0.9992101 0.9984637
## 6-3  0.9986722 0.9995971 0.9986520 0.9987299 0.9994188 0.9980676 0.9974754
## 6-5  0.9990794 0.9987820 1.0000000 0.9993430 0.9988643 0.9982833 0.9977571
## 7-1  0.9984308 0.9985137 1.0000000 1.0000000 0.9992045 0.9990584 0.9991422
## 7-3  0.9981772 0.9990960 1.0000000 0.9995221 1.0000000 0.9987058 0.9978329
## 7-5  0.9994592 0.9992416 1.0000000 1.0000000 1.0000000 0.9992978 0.9992851
## 8-1  0.9977674 0.9990728 0.9989476 0.9975454 0.9992834 0.9977901 0.9977998
## 8-3  0.9971751 0.9989730 1.0000000 0.9978112 1.0000000 0.9975645 0.9988326
## 8-5  0.9983855 0.9984592 1.0000000 0.9994527 0.9991565 0.9985384 0.9979568
## 9-1  0.9992327 0.9995183 0.9994504 0.9994888 1.0000000 0.9986248 0.9994374
## 9-3  0.9979945 1.0000000 1.0000000 0.9962798 1.0000000 0.9987257 0.9989806
## 9-5  0.9983978 0.9994914 0.9994150 0.9989166 0.9983396 0.9990345 0.9988389
##            6-1       6-3       6-5       7-1       7-3       7-5       8-1
## 1-3                                                                       
## 10-1                                                                      
## 10-3                                                                      
## 10-5                                                                      
## 11-1                                                                      
## 11-3                                                                      
## 11-5                                                                      
## 12-1                                                                      
## 12-3                                                                      
## 12-5                                                                      
## 13-1                                                                      
## 13-5                                                                      
## 14-1                                                                      
## 14-5                                                                      
## 15-1                                                                      
## 15-5                                                                      
## 16-1                                                                      
## 16-5                                                                      
## 17-1                                                                      
## 17-5                                                                      
## 18-1                                                                      
## 18-5                                                                      
## 19-1                                                                      
## 19-5                                                                      
## 2-1                                                                       
## 2-3                                                                       
## 2-5                                                                       
## 20-1                                                                      
## 20-5                                                                      
## 21-1                                                                      
## 22-5                                                                      
## 23-1                                                                      
## 23-5                                                                      
## 24-1                                                                      
## 24-5                                                                      
## 3-1                                                                       
## 3-3                                                                       
## 3-5                                                                       
## 5-1                                                                       
## 5-3                                                                       
## 5-5                                                                       
## 6-1                                                                       
## 6-3  0.9149154                                                            
## 6-5  0.9381740 0.9444444                                                  
## 7-1  0.9983760 0.9988088 0.9988085                                        
## 7-3  0.9988709 0.9985253 0.9994660 0.8741663                              
## 7-5  0.9988656 0.9989002 0.9979561 0.9254613 0.9212395                    
## 8-1  0.9988468 0.9984945 0.9983489 0.9981764 0.9991623 1.0000000          
## 8-3  0.9995819 0.9971399 0.9987558 0.9994960 0.9990817 1.0000000 0.9528857
## 8-5  0.9983274 0.9995913 0.9981332 1.0000000 0.9995408 1.0000000 0.9726673
## 9-1  0.9968260 0.9972826 0.9971198 1.0000000 0.9969651 0.9992920 0.9982230
## 9-3  0.9989521 0.9989817 0.9991103 0.9986671 0.9988197 1.0000000 0.9987797
## 9-5  0.9987554 0.9971614 0.9975400 0.9985019 0.9986342 0.9992322 0.9985988
##            8-3       8-5       9-1       9-3
## 1-3                                         
## 10-1                                        
## 10-3                                        
## 10-5                                        
## 11-1                                        
## 11-3                                        
## 11-5                                        
## 12-1                                        
## 12-3                                        
## 12-5                                        
## 13-1                                        
## 13-5                                        
## 14-1                                        
## 14-5                                        
## 15-1                                        
## 15-5                                        
## 16-1                                        
## 16-5                                        
## 17-1                                        
## 17-5                                        
## 18-1                                        
## 18-5                                        
## 19-1                                        
## 19-5                                        
## 2-1                                         
## 2-3                                         
## 2-5                                         
## 20-1                                        
## 20-5                                        
## 21-1                                        
## 22-5                                        
## 23-1                                        
## 23-5                                        
## 24-1                                        
## 24-5                                        
## 3-1                                         
## 3-3                                         
## 3-5                                         
## 5-1                                         
## 5-3                                         
## 5-5                                         
## 6-1                                         
## 6-3                                         
## 6-5                                         
## 7-1                                         
## 7-3                                         
## 7-5                                         
## 8-1                                         
## 8-3                                         
## 8-5  0.9592157                              
## 9-1  0.9975508 0.9985301                    
## 9-3  0.9986009 1.0000000 0.9621309          
## 9-5  0.9984468 0.9994821 0.9417476 0.9716851

Cell type diversity

this data is already log10(inv.simp)

## [[1]]

## 
## [[2]]

## 
## [[3]]

## 
## [[4]]

## 
## [[5]]

## 
## [[6]]

## 
## [[7]]

## 
## [[8]]

## 
## [[9]]

TM diversity

raw diversity

##  1-1  1-3 10-1 10-3 10-5 11-1 11-3 11-5 12-1 12-3 12-5 13-1 13-5 14-1 14-5 15-1 
##  469  372   53  104   79  144  134  212  122  353  565   74   88  402  407   73 
## 15-5 16-1 16-5 17-1 17-5 18-1 18-5 19-1 19-5  2-1  2-3  2-5 20-1 20-5 21-1 22-5 
##   77   86   79  236  271  198  373   82   80  180  143  145  138    9   28   53 
## 23-1 23-5 24-1 24-5  3-1  3-3  3-5  5-1  5-3  5-5  6-1  6-3  6-5  7-1  7-3  7-5 
##    1   84  255  245   28   21   28   91  270  377  327  286  124   35   45   18 
##  8-1  8-3  8-5  9-1  9-3  9-5 
##   23   14    9  210   52  127

Change in diversity

cell type diversity

this data is already log10(inv.simp)

## [[1]]

## 
## [[2]]

## 
## [[3]]

## 
## [[4]]

## 
## [[5]]

## 
## [[6]]

## 
## [[7]]

## 
## [[8]]

## 
## [[9]]

#### BM diversity

raw diversity

##  1-1  1-3 10-1 10-3 10-5 11-1 11-3 11-5 12-1 12-3 12-5 13-1 13-5 14-1 14-5 15-1 
##  469  372   53  104   79  144  134  212  122  353  565   74   88  402  407   73 
## 15-5 16-1 16-5 17-1 17-5 18-1 18-5 19-1 19-5  2-1  2-3  2-5 20-1 20-5 21-1 22-5 
##   77   86   79  236  271  198  373   82   80  180  143  145  138    9   28   53 
## 23-1 23-5 24-1 24-5  3-1  3-3  3-5  5-1  5-3  5-5  6-1  6-3  6-5  7-1  7-3  7-5 
##    1   84  255  245   28   21   28   91  270  377  327  286  124   35   45   18 
##  8-1  8-3  8-5  9-1  9-3  9-5 
##   23   14    9  210   52  127

Change in diversity

cell type diversity

this data is already log10(inv.simp)

## [[1]]

## 
## [[2]]

## 
## [[3]]

## 
## [[4]]

## 
## [[5]]

## 
## [[6]]

## 
## [[7]]

## 
## [[8]]

## 
## [[9]]

clonotype size rarefaction

spectratyping

overlap

similarity validation

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the pre-post tils always strong cluster in overlap/jaccard/morisita 26/9/3/12 consistent, 19 and 7 iffy (7 really low counts)

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morisita looks beautiful, all patients cluster really strongly some mixing with the low 20’s in jaccard and overlap, but overall very strong

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overlap is nearly perfect (just 3til and 3pbmc separate but still have an island of overlap out there), jaccard good but mixes some up, morisita segregates like all the til from nontil

temporal pbmc overlap

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yo jaccard ignores proportions/clones, just based off cdr3s

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Not really any dramatic differences after filtering out the cell types with very few cells Tregs have very low overlap in general, Th2 as well, whereas CD8s have much higher

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Once again, not really strong clinical diffs, maybe lynch higher CD8 act? (which is surprising) and nlr higher CD4 act? then again this is peripheral so not sure what to expect Treg has comparable temporal overlap to naive populations - less large preserved clones?

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all really low counts, but CD8 Activated actually does look lower overlap in nlr though

pbmc-til overlap

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looks like generally stronger 5-7 overlap (but small and not much for any other)

the questionable data shows enrichment towards both extremes with outliers removed though, it looks like just increase in TM overlap for NLR

it kinda looked like something was there, but looks inconclusive

Clonotype cell types

this is erroring right now for me? 08.19 don’t have scaling worked out yet, and this is overall but treg lot of overlap cd4act cd8, cd8exh-act strong, cd4 act-exh?

not much clinical diff, maybe a bit more single in nr more 2+ in nr, more 2 in nlr/maybe l; the high nr outliers are 17

TEMRA distinctness

## [[1]]
## [[1]]$`CD8 TEMRA`
## [1] 127
## 
## [[1]]$Other
## [1] 1878
## 
## 
## [[2]]
## [[2]]$`CD8 TEMRA`
## [1] 108
## 
## [[2]]$Other
## [1] 1753
## 
## 
## [[3]]
## [[3]]$`CD8 TEMRA`
## [1] 14
## 
## [[3]]$Other
## [1] 1348
## 
## 
## [[4]]
## [[4]]$`CD8 TEMRA`
## [1] 98
## 
## [[4]]$Other
## [1] 2039
## 
## 
## [[5]]
## [[5]]$`CD8 TEMRA`
## [1] 73
## 
## [[5]]$Other
## [1] 2440
## 
## 
## [[6]]
## [[6]]$`CD8 TEMRA`
## [1] 122
## 
## [[6]]$Other
## [1] 2363
## 
## 
## [[7]]
## [[7]]$`CD8 TEMRA`
## [1] 136
## 
## [[7]]$Other
## [1] 1631
## 
## 
## [[8]]
## [[8]]$`CD8 TEMRA`
## [1] 261
## 
## [[8]]$Other
## [1] 3503
## 
## 
## [[9]]
## [[9]]$`CD8 TEMRA`
## [1] 37
## 
## [[9]]$Other
## [1] 1385
## 
## 
## [[10]]
## [[10]]$`CD8 TEMRA`
## [1] 72
## 
## [[10]]$Other
## [1] 3259
## 
## 
## [[11]]
## [[11]]$`CD8 TEMRA`
## [1] 194
## 
## [[11]]$Other
## [1] 6061
## 
## 
## [[12]]
## [[12]]$`CD8 TEMRA`
## [1] 56
## 
## [[12]]$Other
## [1] 1724
## 
## 
## [[13]]
## [[13]]$`CD8 TEMRA`
## [1] 89
## 
## [[13]]$Other
## [1] 2158
## 
## 
## [[14]]
## [[14]]$`CD8 TEMRA`
## [1] 222
## 
## [[14]]$Other
## [1] 1003
## 
## 
## [[15]]
## [[15]]$`CD8 TEMRA`
## [1] 181
## 
## [[15]]$Other
## [1] 1268
## 
## 
## [[16]]
## [[16]]$`CD8 TEMRA`
## [1] 107
## 
## [[16]]$Other
## [1] 2582
## 
## 
## [[17]]
## [[17]]$`CD8 TEMRA`
## [1] 147
## 
## [[17]]$Other
## [1] 2837
## 
## 
## [[18]]
## [[18]]$`CD8 TEMRA`
## [1] 74
## 
## [[18]]$Other
## [1] 1962
## 
## 
## [[19]]
## [[19]]$`CD8 TEMRA`
## [1] 84
## 
## [[19]]$Other
## [1] 1930
## 
## 
## [[20]]
## [[20]]$`CD8 TEMRA`
## [1] 267
## 
## [[20]]$Other
## [1] 729
## 
## 
## [[21]]
## [[21]]$`CD8 TEMRA`
## [1] 274
## 
## [[21]]$Other
## [1] 890
## 
## 
## [[22]]
## [[22]]$`CD8 TEMRA`
## [1] 52
## 
## [[22]]$Other
## [1] 456
## 
## 
## [[23]]
## [[23]]$`CD8 TEMRA`
## [1] 111
## 
## [[23]]$Other
## [1] 879
## 
## 
## [[24]]
## [[24]]$`CD8 TEMRA`
## [1] 163
## 
## [[24]]$Other
## [1] 1633
## 
## 
## [[25]]
## [[25]]$`CD8 TEMRA`
## [1] 180
## 
## [[25]]$Other
## [1] 2641
## 
## 
## [[26]]
## [[26]]$`CD8 TEMRA`
## [1] 207
## 
## [[26]]$Other
## [1] 2241
## 
## 
## [[27]]
## [[27]]$`CD8 TEMRA`
## [1] 139
## 
## [[27]]$Other
## [1] 2367
## 
## 
## [[28]]
## [[28]]$`CD8 TEMRA`
## [1] 149
## 
## [[28]]$Other
## [1] 1831
## 
## 
## [[29]]
## [[29]]$`CD8 TEMRA`
## [1] 133
## 
## [[29]]$Other
## [1] 1493
## 
## 
## [[30]]
## [[30]]$`CD8 TEMRA`
## [1] 28
## 
## [[30]]$Other
## [1] 60
## 
## 
## [[31]]
## [[31]]$`CD8 TEMRA`
## [1] 118
## 
## [[31]]$Other
## [1] 2623
## 
## 
## [[32]]
## [[32]]$`CD8 TEMRA`
## [1] 132
## 
## [[32]]$Other
## [1] 2889
## 
## 
## [[33]]
## [[33]]$`CD8 TEMRA`
## [1] 105
## 
## [[33]]$Other
## [1] 3247
## 
## 
## [[34]]
## [[34]]$`CD8 TEMRA`
## [1] 96
## 
## [[34]]$Other
## [1] 2676
## 
## 
## [[35]]
## [[35]]$`CD8 TEMRA`
## [1] 102
## 
## [[35]]$Other
## [1] 1765
## 
## 
## [[36]]
## [[36]]$`CD8 TEMRA`
## [1] 198
## 
## [[36]]$Other
## [1] 1149
## 
## 
## [[37]]
## [[37]]$`CD8 TEMRA`
## [1] 139
## 
## [[37]]$Other
## [1] 1516
## 
## 
## [[38]]
## [[38]]$`CD8 TEMRA`
## [1] 26
## 
## [[38]]$Other
## [1] 376
## 
## 
## [[39]]
## [[39]]$`CD8 TEMRA`
## [1] 123
## 
## [[39]]$Other
## [1] 1965
## 
## 
## [[40]]
## [[40]]$`CD8 TEMRA`
## [1] 189
## 
## [[40]]$Other
## [1] 4564
## 
## 
## [[41]]
## [[41]]$`CD8 TEMRA`
## [1] 216
## 
## [[41]]$Other
## [1] 2488
## 
## 
## [[42]]
## [[42]]$`CD8 TEMRA`
## [1] 203
## 
## [[42]]$Other
## [1] 2684
## 
## 
## [[43]]
## [[43]]$`CD8 TEMRA`
## [1] 90
## 
## [[43]]$Other
## [1] 1096
## 
## 
## [[44]]
## [[44]]$`CD8 TEMRA`
## [1] 190
## 
## [[44]]$Other
## [1] 1717
## 
## 
## [[45]]
## [[45]]$`CD8 TEMRA`
## [1] 178
## 
## [[45]]$Other
## [1] 2109
## 
## 
## [[46]]
## [[46]]$`CD8 TEMRA`
## [1] 66
## 
## [[46]]$Other
## [1] 499
## 
## 
## [[47]]
## [[47]]$`CD8 TEMRA`
## [1] 92
## 
## [[47]]$Other
## [1] 2131
## 
## 
## [[48]]
## [[48]]$`CD8 TEMRA`
## [1] 266
## 
## [[48]]$Other
## [1] 1495
## 
## 
## [[49]]
## [[49]]$`CD8 TEMRA`
## [1] 114
## 
## [[49]]$Other
## [1] 1643
## 
## 
## [[50]]
## [[50]]$`CD8 TEMRA`
## [1] 107
## 
## [[50]]$Other
## [1] 1958
## 
## 
## [[51]]
## [[51]]$`CD8 TEMRA`
## [1] 31
## 
## [[51]]$Other
## [1] 849
## 
## 
## [[52]]
## [[52]]$`CD8 TEMRA`
## [1] 80
## 
## [[52]]$Other
## [1] 1715
## 
## 
## [[53]]
## [[53]]$`CD8 TEMRA`
## [1] 158
## 
## [[53]]$Other
## [1] 1530
## 
## 
## [[54]]
## [[54]]$`CD8 TEMRA`
## [1] 71
## 
## [[54]]$Other
## [1] 1542
## 
## 
## [[55]]
## [[55]]$`CD8 TEMRA`
## [1] 184
## 
## [[55]]$Other
## [1] 4134
## 
## 
## [[56]]
## [[56]]$`CD8 TEMRA`
## [1] 227
## 
## [[56]]$Other
## [1] 3287
## 
## 
## [[57]]
## [[57]]$`CD8 TEMRA`
## [1] 80
## 
## [[57]]$Other
## [1] 2436
## 
## 
## [[58]]
## [[58]]$`CD8 TEMRA`
## [1] 72
## 
## [[58]]$Other
## [1] 3540
## 
## 
## [[59]]
## [[59]]$`CD8 TEMRA`
## [1] 78
## 
## [[59]]$Other
## [1] 2594
## 
## 
## [[60]]
## [[60]]$`CD8 TEMRA`
## [1] 206
## 
## [[60]]$Other
## [1] 3582
## 
## 
## [[61]]
## [[61]]$`CD8 TEMRA`
## [1] 216
## 
## [[61]]$Other
## [1] 2598

still not entirely sure about the mechanics of vegdist could still be a size effect of the temra, haven’t done downsampling also mean or median for the column version?

Cell counts

Main

got some interesting ones, 25 is just 14, 15 strong 23/5, 23-1 is just 6 cells, 21-1 is 200 cells specific clusts - 3 (l high - temra right),8 (nlr lo - cd8 naive), 12 (nlr hi, cd4 activated ish, center top), 16 (nlr hi - dead?), 18(nlr hi,l lo, cd4 naive),21 (nlr hi - cd4 early?), 24 (l lo,cd8-4 transition), 29 (l lo - left gdt), ldat clusts - 4(nlr lo-cd14mono),9(nlr hi-cd16 mono),19(l lo-cdc),21(nlr hi-cd16nk.2),22(l lo-cd56 nk),26(nlr hi-pdc),28(l lo,nlr hi-mono??),29(l hi-plasma),31(l lo-progenitor),32(l lo-b/mono) hm, half of GDT have TCR ab sequences

That’s actually fire really clean for increase in nlr/nr exh/cycling, decrease/lower MAIT CD8 CM/Th2 increase to meet in lynch decreasing trend for all in TEM/TEMRA, increasing treg nlr low cd8 naive, increase th1

TM composition

Proportion TM

## [[1]]

## 
## [[2]]

## 
## [[3]]

Lynch has higher prop of clones TM, decreases over time

## [[1]]

## 
## [[2]]

## 
## [[3]]

lynch highest prop TM, NLR second NLR is a lot more TM porpotion increase while others decrease But none of this translates to any pattern in change in TM clonality this could also be the result of sample size of pbmc and til - manual jaccard is better?

could do proportion of TMs for each by cell type or proportional composition of TMs for clinical by cell type and then uhhh raref TMs or actually that’s more div stuff

CD8 stuff

no real overall trends ##### clonality